www.nature.com/scientificreports OPEN The same domain of Su(Hw) is required for enhancer blocking and direct promoter repression Received: 6 December 2018 Larisa Melnikova1, Pavel Elizar’ev2, Maksim Erokhin2, Varvara Molodina1, Darya Chetverina 2, Accepted: 14 March 2019 Margarita Kostyuchenko1, Pavel Georgiev2 & Anton Golovnin 1 Published: xx xx xxxx Suppressor of Hairy-wing [Su(Hw)] is a DNA-binding architectural protein that participates in the organization of insulators and repression of promoters in Drosophila. This protein contains acidic regions at both ends and a central cluster of 12 zinc fnger domains, some of which are involved in the specifc recognition of the binding site. One of the well-described in vivo function of Su(Hw) is the repression of transcription of neuronal genes in oocytes. Here, we have found that the same Su(Hw) C-terminal region (aa 720–892) is required for insulation as well as for promoter repression. The best characterized partners of Su(Hw), CP190 and Mod(mdg4)-67.2, are not involved in the repression of neuronal genes. Taken together, these results suggest that an unknown protein or protein complex binds to the C-terminal region of Su(Hw) and is responsible for the direct repression activity of Su(Hw). High-resolution chromosome conformation capture techniques have provided evidence that regulatory elements form loops that are essential for gene regulation in higher eukaryotes1–6. In particular enhancers can activate target promoters at large distances (up to hundreds of kb in some cases), which raises the question of the mech- anisms regulating such long-distance enhancer–promoter interactions. More than 25 years ago, a special class of regulatory elements, named insulators, was suggested to delimit the activity of enhancers7–12. Insulators are defned as regulatory elements that disrupt the communication between an enhancer and a promoter when inserted between them. Some insulator complexes contribute to higher-order organization of chromatin in topo- logically associated domains that are fundamental elements of the eukaryotic genomic structure13,14. One of the frst insulators was identifed in the gypsy retrotransposon, whose integration into genes ofen resulted in inactivation of enhancers that were separated from promoters by the gypsy insertion15–19. Te phe- notypes of the gypsy-induced mutations were suppressed by inactivation of the gene encoding the Suppressor of hairy wing protein [Su(Hw)]20. Te gypsy insulator consists of 12 reiterated binding sites for Su(Hw)21,22. Today, Su(Hw) is one of the best characterized insulator proteins. It has been shown that artifcial reiterated binding sites for Su(Hw) or gypsy insulator can block various enhancers at all stages of Drosophila development21,23–27. Te Su(Hw) protein contains the N-terminal region involved in the interaction with CP190, an array of 12 C2H2-type zinc fnger domains, and the C-terminal region (aa 716–892) responsible for enhancer blocking activity28–32. Several Su(Hw) partners were identifed, including Mod(mdg4), CP190, ENY2, Shep, Rump, and HIPP128,33–38. Mod(mdg4)-67.2 is one of the isoforms encoded by the mod(mdg4) locus39,40. Te Mod(mdg4)-67.2 protein contains the N-terminal BTB/POZ domain and glutamine-rich (Q-rich) region which is common to all isoforms and the unique C-terminal region that is required for interaction with the 716–892 aa region of Su(Hw)28,31,34. Te BTB and Q-rich domains of the Mod(mdg4)-67.2 interact with the M domain of CP190 and the N-terminal region of Su(Hw) (aa 1–238), respectively31. Te functions of Mod(mdg4)-67.2 are as yet unknown, except for its participation in recruiting the Su(Hw) complex to specifc chromatin sites and masking the repression activity of Su(Hw)31,41,42. Te CP190 protein contains the N-terminal BTB domain that forms stable homodimers43–46. Te BTB domain interacts with two adjacent regions at the Su(Hw) N-terminus, which is essential for CP190 recruitment to Su(Hw) sites32. CP190 is involved in the recruitment of several transcriptional complexes to chromatin, including the NURF, dREAM, and SAGA complexes47,48. CP190 has major efects on chromatin, such as the depletion of 1Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia. 2Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia. Correspondence and requests for materials should be addressed to P.G. (email: [email protected]) or A.G. (email: [email protected]) SCIENTIFIC REPORTS | (2019) 9:5314 | https://doi.org/10.1038/s41598-019-41761-6 1 www.nature.com/scientificreports/ www.nature.com/scientificreports nucleosomes and the prevention of heterochromatin expansion49. Similar to CP190, ENY2 is recruited to chro- matin by interacting with Su(Hw) and participates in the boundary function of Su(Hw), which protects active genes from silencing36. Shep and Rump are the RNA binding proteins that function as negative regulators of the Su(Hw) enhancer blocking activity35,37. HIPP1 (CG3680) was identifed as possible partner of Su(Hw) in a recent screen of proteins interacting with HP1, one of the main heterochromatin proteins33. Strong co-localization of HIPP1 and Su(Hw) sites suggests that these proteins are in the same complex33. In previous genome-wide studies, three classes of the Su(Hw) binding regions have been identifed, which are characterized by the binding of Su(Hw) alone (SBS-O), both Su(Hw) and CP190 (SBS-C), or three proteins Su(Hw)/CP190/Mod(mdg4)-67.2 (SBS-CM)50–53. It has been shown that many SBS-O sites are involved in tran- scriptional repression52,54. Te function of Su(Hw) as transcriptional repressor is required for female germline development54 and for sustained male fertility55. Here, we made an attempt to identify Su(Hw) domains involved in the repression of several neuronal genes in the ovary. We found that the same C-terminal region (aa 720–892) in Su(Hw) is required for enhancer blocking and for promoter repression. Results Model system for studying Su(Hw)-dependent repression. As shown previously, Su(Hw) is involved in the repression of many neural genes in the ovary54,56. Tese genes contain binding sites for Su(Hw) in promoter regions, suggesting the involvement of this protein in direct repression of transcription. To further character- ize Su(Hw) domains involved in repression, we selected fve representative neural genes whose promoters are bound by Su(Hw) alone (Rph, cg32017, and Hs3st-A), by Su(Hw) and CP190 (Syn2), or by Su(Hw), CP190, and Mod(mdg4)-67.2 (mAcR-60C) (Fig. 1a). Using ChIP, we confrmed the binding of the insulator proteins to the promoters in the ovaries and heads of females (Fig. 1b). Interestingly, ChIP with a common antibody against all Mod(mdg4) isoforms showed an enrichment of Mod(mdg4) at the promoters. However, Mod(mdg4)-67.2 binds only to the Su(Hw) site at the mAcR-60C promoter, suggesting that another Mod(mdg4) isoform was recruited to other promoters by an unknown DNA-bound protein. In general, the observed patterns of Su(Hw), CP190, and Mod(mdg4)-67.2 recruitment to the tested promoters in the ovaries and heads were similar, which is in agree- ment with the previous observation that these proteins stably bind to their sites in diferent Drosophila tissues and cell lines51–54. We then compared the expression of the model genes in the heads and ovaries of females (Fig. 2a). As expected, the model genes were repressed in the ovaries and actively transcribed in the heads. To confrm the role of Su(Hw) in gene repression, we examined the expression of the model genes in the su(Hw)− background. In the absence of the Su(Hw) protein, transcription from the tested genes proved to be increased 10- to 20-fold in the ovaries, while its level in the heads remained unchanged (Fig. 2b). Taken together, these results confrm that the selected genes provide a good model system for the study of Su(Hw)-mediated repression in the ovaries. Tissue-specifc repression of model genes depends on the presence of Su(Hw) binding sites in promoters. Tere are two possible mechanisms explaining how the Su(Hw) protein can repress the promot- ers: (1) Su(Hw) competes for the binding site with a transcription factor that activates transcription; (2) Su(Hw) recruits a tissue-specifc complex that is responsible for repression. To test these alternative models, we mutated the Su(Hw) binding sites in the promoters of the mAcR-60C and Rph genes (Fig. 3a). Te lacZ gene was used as a reporter to test the activity of the promoters, and the mini-white gene, which determines eye pigmentation, was used as a marker to select positive transgenic lines. Te tested genes were cloned with the attB site to allow site-specifc integration with the phiC31 integrase system57. Te constructs were inserted in the same genomic region 38D. Te RT-qPCR analysis in the ovaries showed that mutational inactivation of Su(Hw) binding sites led to an increase in transcription, compared to the wild-type level, by a factor of 4 for mAcR-60C and by a factor of 6 for Rph (Fig. 3b). At the same time, the efect of mutations in the promoters on transcription of the reporter in the heads lacked statistical signifcance. Tese results argue against the model that Su(Hw) masks binding site for a transcriptional activator in the promoters. We also tested whether the overexpression of Su(Hw) can afect transcription of the model genes in the heads.